1xwp

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[[Image:1xwp.gif|left|200px]]
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{{STRUCTURE_1xwp| PDB=1xwp | SCENE= }}
{{STRUCTURE_1xwp| PDB=1xwp | SCENE= }}
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'''Solution structure of AUCGCA loop'''
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===Solution structure of AUCGCA loop===
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==Overview==
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A high affinity RNA aptamer (APT58, 58 nt long) against mammalian initiation factor 4A (eIF4A) requires nearly its entire nucleotide sequence for efficient binding. Since splitting either APT58 or eIF4A into two domains diminishes the affinity for each other, it is suggested that multiple interactions or a global interaction between the two molecules accounts for the high affinity. To understand the structural basis of APT58's global recognition of eIF4A, we determined the solution structure of two essential nucleotide loops (AUCGCA and ACAUAGA) within the aptamer using NMR spectroscopy. The AUCGCA loop is stabilized by a U-turn motif and contains a non-canonical A:A base pair (the single hydrogen bond mismatch: Hoogsteen/Sugar-edge). On the other hand, the ACAUAGA loop is stabilized by an AUA tri-nucleotide loop motif and contains the other type of A:A base pair (single hydrogen bond mismatch: Watson-Crick/Watson-Crick). Considering the known structural and functional properties of APT58, we propose that the AUCGCA loop is directly involved in the interaction with eIF4A, while the flexibility of the ACAUAGA loop is important to support this interaction. The Watson-Crick edges of C7 and C9 in the AUCGCA loop may directly interact with eIF4A.
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(as it appears on PubMed at http://www.pubmed.gov), where 15687383 is the PubMed ID number.
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{{ABSTRACT_PUBMED_15687383}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XWP OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XWP OCA].
==Reference==
==Reference==
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[[Category: Sakamoto, T.]]
[[Category: Sakamoto, T.]]
[[Category: Hairpin loop]]
[[Category: Hairpin loop]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 15:36:08 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 20:54:15 2008''

Revision as of 17:54, 27 July 2008

Image:1xwp.png

Template:STRUCTURE 1xwp

Solution structure of AUCGCA loop

Template:ABSTRACT PUBMED 15687383

About this Structure

Full experimental information is available from OCA.

Reference

NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A., Sakamoto T, Oguro A, Kawai G, Ohtsu T, Nakamura Y, Nucleic Acids Res. 2005 Feb 1;33(2):745-54. Print 2005. PMID:15687383

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